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X-RAY DIFFRACTION
Materials and Methods page
1N6Y
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 298.0
    Details 25% polyethylene glycol (PEG) 8000, 0.2 M ammonium sulphate, 0.1 M Tris buffer, pH 8, and 100 mM benzylamine, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.24 α = 90
    b = 56.75 β = 90
    c = 66.2 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2001-06-13
     
    Diffraction Radiation
    Monochromator Si111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength List 0.9763
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.4
    Resolution(Low) 42
    Number Reflections(All) 41043
    Number Reflections(Observed) 40971
    Percent Possible(Observed) 99.83
    R Merge I(Observed) 0.05
    B(Isotropic) From Wilson Plot 12.31
    Redundancy 13.1
     
    High Resolution Shell Details
    Resolution(High) 1.4
    Resolution(Low) 1.47
    Percent Possible(All) 97.4
    R Merge I(Observed) 0.312
    Mean I Over Sigma(Observed) 2.7
    Redundancy 11.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method RIP - Radiation-Damage Induced Phasing
    reflnsShellList 1.4
    Resolution(Low) 42.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 40971
    Number of Reflections(Observed) 40971
    Number of Reflections(R-Free) 2061
    Percent Reflections(Observed) 99.83
    R-Factor(All) 0.142
    R-Factor(Observed) 0.142
    R-Work 0.14051
    R-Free 0.17021
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Anisotropic for protein and ligands. Water molecules are refined isotropic
    Mean Isotropic B Value 14.552
    Anisotropic B[1][1] -0.1
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.08
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4
    Shell Resolution(Low) 1.436
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2804
    R-Factor(R-Work) 0.194
    R-Factor(R-Free) 0.239
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 7.18
    r_sphericity_free 1.774
    r_rigid_bond_restr 1.419
    r_scangle_it 4.876
    r_bond_refined_d 0.017
    r_angle_refined_deg 1.633
    r_dihedral_angle_1_deg 6.285
    r_chiral_restr 0.125
    r_gen_planes_refined 0.009
    r_nbd_refined 0.199
    r_xyhbond_nbd_refined 0.125
    r_symmetry_vdw_refined 0.179
    r_symmetry_hbond_refined 0.156
    r_mcbond_it 1.758
    r_mcangle_it 2.799
    r_scbond_it 3.656
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1629
    Nucleic Acid Atoms 0
    Heterogen Atoms 25
    Solvent Atoms 288
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) PRODC
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Solution SHELXD, SHARP
    Structure Refinement REFMAC 5.1.24
     
    Software
    refinement REFMAC version: 5.1.24
    model building sharp
    model building shelxd
    data reduction SCALA
    data collection prodc